gcta 1.26.0

GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits. GCTA currently supports the analyses as follows.

  • GRM: estimating the genetic relationships among individuals in GWAS data;
  • Estimating the inbreeding coefficients of individuals in GWAS data;
  • GREML: estimating the proportion of variance in a phenotype explained by all GWAS SNPs (i.e. the SNP-based heritability);
  • Partitioning the genetic variance onto individual chromosomes, MAF bins or functional categories;
  • Estimating the genetic variance attributed to chromosome X, and testing for the effect of dosage compensation;
  • GREMLd: estimating the dominance variance in unrelated individuals using GWAS data;
  • Bivariate GREML: estimating the genetic correlation between two traits (diseases) using GWAS data;
  • PCA analysis and estimation of Fst in GWAS data
  • Computing LD scores and searching for LD friends for a list of target SNPs;
  • Simulating a phenotype based on GWAS data;
  • Conditional & joint (COJO) analysis of GWAS summary statistics without individual level genotype data;
  • Mixed linear model association analysis;
  • Gene- or set-based association analysis;
  • Sumamry-data based BLUP;
  • Haseman-Elston regression to estimate the the SNP-based heritability for a trait and the genetic correlation between two traits.

Accessing the software

To load the module:

$ module load apps/gcta/1.26.0

The command to run the analysis for this application is:

$ gcta64

View the documentation on basic options to see what this application expects.

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the gcta website for more information regarding this application.

Last modified: 11 September 2017